Omar Minaya finally sent his old friend Tony Bernazard packing today, after a week of reports that the former vice president of player development had gotten into numerous confrontations with both players and other staff members.

The general manager said repeatedly that the firing of Bernazard, who has long been a lightning rod for criticism, was the result of an investigation by the Mets’ human relations department — but that the final decision was his.

“I met with Tony Bernazard [on Sunday] and showed him the facts that were there,” said Minaya, who told Bernazard of the firing today. “When all is said and done, I made my recommendation to ownership.”

That followed reports about the 52-year-old challenging players on the team’s Double A affiliate, getting into an altercation with closer Francisco Rodriguez, who declined comment before the Mets beat the Rockies at Citi Field tonight, and shouting at another team employee in public. But both Minaya and owner Jeff Wilpon said that the internal investigation began before any reports surfaced.

“There were things [done] that were against what the organization believes in,” said Minaya, who was practically incoherent at times and repeatedly talked of Bernazard’s “interpersonal” issues. “It was multiple things.”

Minaya refused to go into specifics.

“All the things that have been in the public are not exactly how they happened, but I’m not getting into details of that,” said Minaya, who also said that he was initially skeptical of some of the early reports from Daily News Mets beat writer Adam Rubin, who Minaya said had “lobbied” him for a job similar to Bernazard’s in the past.

“I was surprised by some of the things in [the HR] report,” Minaya said. “I had to be surprised, of course, some of things I did not know about.”

The entire episode also calls into question Minaya’s security within the organization. Minaya, who admitted he was at fault for what had happened within the organization, was close to Bernazard.

“It does reflect upon my watch and I take full responsibility,” said Minaya, who claimed not to know about all the details that have come out recently about Bernazard.

It added up to yet another bad day for a franchise going through a terrible season.

“You never like for these things to happen,” Minaya said. “So it’s not good for organization. But we will move on.”

Minaya, who said he intends to fill Bernazard’s job from within, added that he was “completely satisfied” with the way Bernazard developed the Mets’ system.

“Tony Bernazard is a person I have a lot of respect for,” Minaya said. “He is a hard worker, a very talented baseball man. I know that contrary to what people think, as

far as our player development system, we have a lot of players he’s been a big part of. He’s been a big part of our success.

“I say this, we’re not playing good right now, we have injuries, but before this year when the year started we were fourth in wins in the past four years.”

The fact remains that Bernazard, who was thought by many to be behind Willie Randolph’s firing as manager last year, clearly had problems throughout the organization that led to the Mets having to fire him.

“We owe it to ourselves to review them,” Minaya said of the way the club operates. “The bottom line is we’re gonna make some changes internally.”

Minaya said he didn’t regret letting Bernazard have the access or power that he did.

“Not at all,” Minaya said. “Tony worked well with me and the whole staff.”

Except, of course, for the ones at whom he screamed and cursed.

“I know it’s out there that Tony had a special relationship with Jeff Wilpon,” Minaya said. “That’s not true. Me and Jeff work very well.”

That can’t be said for Minaya and Bernazard anymore.

“I do believe we have a very good minor league system,” Minaya said. “We have good young players and I believe in our minor leagues.”